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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 12-41070009-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=41070009&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 6,
"criteria": [
"BP4_Moderate",
"BS1"
],
"effects": [
"missense_variant"
],
"gene_symbol": "CNTN1",
"hgnc_id": 2171,
"hgvs_c": "c.3031G>A",
"hgvs_p": "p.Gly1011Ser",
"inheritance_mode": "AR,Unknown",
"pathogenic_score": 0,
"score": -6,
"transcript": "NM_001843.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS1",
"acmg_score": -6,
"allele_count_reference_population": 234,
"alphamissense_prediction": null,
"alphamissense_score": 0.2006,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.39,
"chr": "12",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Compton-North congenital myopathy,Inborn genetic diseases,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.08469843864440918,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1018,
"aa_ref": "G",
"aa_start": 1011,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5667,
"cdna_start": 3261,
"cds_end": null,
"cds_length": 3057,
"cds_start": 3031,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "NM_001843.4",
"gene_hgnc_id": 2171,
"gene_symbol": "CNTN1",
"hgvs_c": "c.3031G>A",
"hgvs_p": "p.Gly1011Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000551295.7",
"protein_coding": true,
"protein_id": "NP_001834.2",
"strand": true,
"transcript": "NM_001843.4",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1018,
"aa_ref": "G",
"aa_start": 1011,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5667,
"cdna_start": 3261,
"cds_end": null,
"cds_length": 3057,
"cds_start": 3031,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "ENST00000551295.7",
"gene_hgnc_id": 2171,
"gene_symbol": "CNTN1",
"hgvs_c": "c.3031G>A",
"hgvs_p": "p.Gly1011Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001843.4",
"protein_coding": true,
"protein_id": "ENSP00000447006.1",
"strand": true,
"transcript": "ENST00000551295.7",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1018,
"aa_ref": "G",
"aa_start": 1011,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5507,
"cdna_start": 3110,
"cds_end": null,
"cds_length": 3057,
"cds_start": 3031,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "ENST00000347616.5",
"gene_hgnc_id": 2171,
"gene_symbol": "CNTN1",
"hgvs_c": "c.3031G>A",
"hgvs_p": "p.Gly1011Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000325660.3",
"strand": true,
"transcript": "ENST00000347616.5",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1007,
"aa_ref": "G",
"aa_start": 1000,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3328,
"cdna_start": 3072,
"cds_end": null,
"cds_length": 3024,
"cds_start": 2998,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "ENST00000348761.2",
"gene_hgnc_id": 2171,
"gene_symbol": "CNTN1",
"hgvs_c": "c.2998G>A",
"hgvs_p": "p.Gly1000Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000261160.3",
"strand": true,
"transcript": "ENST00000348761.2",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1028,
"aa_ref": "G",
"aa_start": 1021,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5053,
"cdna_start": 3137,
"cds_end": null,
"cds_length": 3087,
"cds_start": 3061,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "ENST00000901032.1",
"gene_hgnc_id": 2171,
"gene_symbol": "CNTN1",
"hgvs_c": "c.3061G>A",
"hgvs_p": "p.Gly1021Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000571091.1",
"strand": true,
"transcript": "ENST00000901032.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1018,
"aa_ref": "G",
"aa_start": 1011,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5775,
"cdna_start": 3372,
"cds_end": null,
"cds_length": 3057,
"cds_start": 3031,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 25,
"exon_rank_end": null,
"feature": "ENST00000901030.1",
"gene_hgnc_id": 2171,
"gene_symbol": "CNTN1",
"hgvs_c": "c.3031G>A",
"hgvs_p": "p.Gly1011Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000571089.1",
"strand": true,
"transcript": "ENST00000901030.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1018,
"aa_ref": "G",
"aa_start": 1011,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5163,
"cdna_start": 3247,
"cds_end": null,
"cds_length": 3057,
"cds_start": 3031,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "ENST00000901031.1",
"gene_hgnc_id": 2171,
"gene_symbol": "CNTN1",
"hgvs_c": "c.3031G>A",
"hgvs_p": "p.Gly1011Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000571090.1",
"strand": true,
"transcript": "ENST00000901031.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1018,
"aa_ref": "G",
"aa_start": 1011,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6073,
"cdna_start": 3669,
"cds_end": null,
"cds_length": 3057,
"cds_start": 3031,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "ENST00000959376.1",
"gene_hgnc_id": 2171,
"gene_symbol": "CNTN1",
"hgvs_c": "c.3031G>A",
"hgvs_p": "p.Gly1011Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629435.1",
"strand": true,
"transcript": "ENST00000959376.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1007,
"aa_ref": "G",
"aa_start": 1000,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5477,
"cdna_start": 3074,
"cds_end": null,
"cds_length": 3024,
"cds_start": 2998,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "NM_175038.2",
"gene_hgnc_id": 2171,
"gene_symbol": "CNTN1",
"hgvs_c": "c.2998G>A",
"hgvs_p": "p.Gly1000Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_778203.1",
"strand": true,
"transcript": "NM_175038.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1018,
"aa_ref": "G",
"aa_start": 1011,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5631,
"cdna_start": 3225,
"cds_end": null,
"cds_length": 3057,
"cds_start": 3031,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "XM_005268651.3",
"gene_hgnc_id": 2171,
"gene_symbol": "CNTN1",
"hgvs_c": "c.3031G>A",
"hgvs_p": "p.Gly1011Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005268708.1",
"strand": true,
"transcript": "XM_005268651.3",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1018,
"aa_ref": "G",
"aa_start": 1011,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8784,
"cdna_start": 6378,
"cds_end": null,
"cds_length": 3057,
"cds_start": 3031,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "XM_006719241.3",
"gene_hgnc_id": 2171,
"gene_symbol": "CNTN1",
"hgvs_c": "c.3031G>A",
"hgvs_p": "p.Gly1011Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006719304.1",
"strand": true,
"transcript": "XM_006719241.3",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1018,
"aa_ref": "G",
"aa_start": 1011,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5770,
"cdna_start": 3364,
"cds_end": null,
"cds_length": 3057,
"cds_start": 3031,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 25,
"exon_rank_end": null,
"feature": "XM_011537926.4",
"gene_hgnc_id": 2171,
"gene_symbol": "CNTN1",
"hgvs_c": "c.3031G>A",
"hgvs_p": "p.Gly1011Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011536228.1",
"strand": true,
"transcript": "XM_011537926.4",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1018,
"aa_ref": "G",
"aa_start": 1011,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8806,
"cdna_start": 6400,
"cds_end": null,
"cds_length": 3057,
"cds_start": 3031,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "XM_011537927.3",
"gene_hgnc_id": 2171,
"gene_symbol": "CNTN1",
"hgvs_c": "c.3031G>A",
"hgvs_p": "p.Gly1011Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011536229.1",
"strand": true,
"transcript": "XM_011537927.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 512,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000548481.1",
"gene_hgnc_id": 2171,
"gene_symbol": "CNTN1",
"hgvs_c": "n.*106G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000449517.1",
"strand": true,
"transcript": "ENST00000548481.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 512,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000548481.1",
"gene_hgnc_id": 2171,
"gene_symbol": "CNTN1",
"hgvs_c": "n.*106G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000449517.1",
"strand": true,
"transcript": "ENST00000548481.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs200796487",
"effect": "missense_variant",
"frequency_reference_population": 0.00014499866,
"gene_hgnc_id": 2171,
"gene_symbol": "CNTN1",
"gnomad_exomes_ac": 225,
"gnomad_exomes_af": 0.000153924,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 9,
"gnomad_genomes_af": 0.0000591934,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not provided|Compton-North congenital myopathy|Inborn genetic diseases",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.43,
"pos": 41070009,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.113,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.019999999552965164,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.02,
"transcript": "NM_001843.4"
}
]
}